That will be caught, due to the fixed relationship between PID and IVs. But of course there's nothing to stop PokeSav changing the PID as well (though whether it has the feature I don't know). Pokesav has access to the entire save file, there's nowhere for any other data to 'hide'.
Yeah, I was wondering about that. But, you can reset the PIDs with PokeSav, so unless there is some further invisible data that hackers don't know of but Nintendo does, someone could use PokeSav to RNG their Pokemon. Ew...
There is I believe some data about Pokemon with an unknown purpose, which may be to help Nintendo's hack checks. But were its purpose and calculation discovered, the check would be defeated. It's like DRM - always going to be cracked, the question is when not if. From Nintendo's point of view, they only need reliable hack checks for a game until the next one comes out. It's possible the newer 4th gen games contain anti-hacking code the older ones don't, and that might be one reason VGC requires the latest games. (The others being the overt new features, and cynically to make people buy the new games).
I pegged it to be that Nintendo just wanted people to buy the new games; last year, before GSDS was released, Platinum was the game needed to play in the tourney, IIRC.
I guess maybe I DON'T have to worry too much about IV-hacked Pokemon versus RNG'd Pokemon then?